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Took me forever to figure out how to get Darkplaces to run.
It reminded me that --no matter how clearly you think you are explaining something, there's always someone who won't understand.
In this case that someone was me.

After messing with trying to get this game working for QUITE SOME TIME I finally realized that all you need to do...
Is to have the folder "id1" from an actual Quake install (on windows) in the Darkplaces folder.
The folder with it's quake data.
This can be from the full game or from the shareware version.
In the case of the latter you'll only be able to play the first level.

And just like with Transfusion I had to compile the engine myself.
As I said before this is--I think--due to some problem peculiar to debian concerning the opengl library.

Fun game. Now if I could only get my roommates to play a little deathmatch over the home network...

The download comes with pre-compiled linux engine binaries.
The problem I ran into was that they would crash.
I think this is due to something peculiar about the opengl library. Something about debian in particular, so if you're using another distro as like as not they'll just work for you.
But like I was saying, they crashed:

The source itself is in another zip file inside the first one. Unzip that one, cd into the directory, then:

make sdl-release

If you have the dependencies already (I think I had to apt-get install the sdl header files) it should build ok.

Copy the resulting engine file "darkplaces-sdl" to your Transfusion game directory. Since this is an unmodified darkplaces engine you have to start it with a funky command line in order to actually play transfusion:

./darkplaces-sdl -game basetf +map bb3 -listen 8

This will start Transfusion with the bodies map (one of my favs).
The -listen 8 bit at the end is to enable you to have some bots to play in the game.
The single player version of the game is still in development, but multiplayer works and if you're not going to play online you can fire up a few bots after the game loads --just hit the "page up" key. I like playing with all eight bots. Makes for some fast and furious action. Of course I kick their asses. They're just bots.
But sometimes they surprise me...

I want to thank the guys in #qblood on irc.gamesurge.net for helping me figure this out.

Install the shareware version on some windows pc and copy the DUKE3D.GRP to your linux box somehow.
You can also use the duke3d.cfg that you get, just be sure to change the screen res to 1024x768 (better just to use that gentoo file...)
I tested it the DUKE3D.GRP from the full 1.3 version --it works.
But with the Atomic Edition you get that extra forth set of levels.
So if you have a copy of Duke Nukem Atomic Edition laying around you're better off using that.

DEFS.CON, GAME.CON, USER.CON
read the docs that come with the source from CVS.
These files are in there somewhere (after compiling it), and you need to put them in the same directory with DUKE3D.GRP and duke3d and they need to have uppercase names.
I put everything in /usr/local/games/duke3d

That's pretty much it.
I made a launcher script too.
Put it on a button in the launcher gizmo in xfce4:

#!bin/sh

cd /usr/local/games/duke3d #put all those files in here

./duke3d

I even found a duke icon somewhere and put it on the launcher.

Oh yea... for those of you still stuck on windows (everybody else I guess) you can do this one instead: